Dataset Information

Comparative Transcriptomics Among Four White Pine Species.

ABSTRACT: Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus The populations of many Strobus species are challenged by native and introduced pathogens, native insects, and abiotic factors. RNA from the needles of western white pine (Pinus monticola), limber pine (Pinus flexilis), whitebark pine (Pinus albicaulis), and sugar pine (Pinus lambertiana) was sampled, Illumina short read sequenced, and de novo assembled. The assembled transcripts and their subsequent structural and functional annotations were processed through custom pipelines to contend with the challenges of non-model organism transcriptome validation. Orthologous gene family analysis of over 58,000 translated transcripts, implemented through Tribe-MCL, estimated the shared and unique gene space among the four species. This revealed 2025 conserved gene families, of which 408 were aligned to estimate levels of divergence and reveal patterns of selection. Specific candidate genes previously associated with drought tolerance and white pine blister rust resistance in conifers were investigated.

SUBMITTER: Baker EAG

PROVIDER: S-EPMC5940140 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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Comparative Transcriptomics Among Four White Pine Species.

Baker Ethan A G EAG Wegrzyn Jill L JL Sezen Uzay U UU Falk Taylor T Maloney Patricia E PE Vogler Detlev R DR Delfino-Mix Annette A Jensen Camille C Mitton Jeffry J Wright Jessica J Knaus Brian B Rai Hardeep H Cronn Richard R Gonzalez-Ibeas Daniel D Vasquez-Gross Hans A HA Famula Randi A RA Liu Jun-Jun JJ Kueppers Lara M LM Neale David B DB

G3 (Bethesda, Md.) 20180504 5

Conifers are the dominant plant species throughout the high latitude boreal forests as well as some lower latitude temperate forests of North America, Europe, and Asia. As such, they play an integral economic and ecological role across much of the world. This study focused on the characterization of needle transcriptomes from four ecologically important and understudied North American white pines within the Pinus subgenus Strobus The populations of many Strobus species are c ...[more]

PMID: 29559535

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Project description:BackgroundPetal nectar spurs, which facilitate pollination through animal attraction and pollen placement, represent a key innovation promoting diversification in the genus Aquilegia (Ranunculaceae). Identifying the genetic components that contribute to the development of these three-dimensional structures will inform our understanding of the number and types of genetic changes that are involved in the evolution of novel traits. In a prior study, gene expression between two regions of developing petals, the laminar blade and the spur cup, was compared at two developmental stages in the horticultural variety A. coerulea 'Origami'. Several hundred genes were differentially expressed (DE) between the blade and spur at both developmental stages. In order to narrow in on a set of genes crucial to early spur formation, the current study uses RNA sequencing (RNAseq) to conduct comparative expression analyses of petals from five developmental stages between four Aquilegia species, three with morphologically variable nectar spurs, A. sibirica, A. formosa, and A. chrysantha, and one that lacks nectar spurs, A. ecalcarata.ResultsPetal morphology differed increasingly between taxa across the developmental stages assessed, with petals from all four taxa being indistinguishable pre-spur formation at developmental stage 1 (DS1) and highly differentiated by developmental stage 5 (DS5). In all four taxa, genes involved in mitosis were down-regulated over the course of the assessed developmental stages, however, many genes involved in mitotic processes remained expressed at higher levels later in development in the spurred taxa. A total of 690 genes were identified that were consistently DE between the spurred taxa and A. ecalcarata at all five developmental stages. By comparing these genes with those identified as DE between spur and blade tissue in A. coerulea 'Origami', a set of only 35 genes was identified that shows consistent DE between petal samples containing spur tissue versus those without spur tissue.ConclusionsThe results of this study suggest that expression differences in very few loci are associated with the presence and absence of spurs. In general, it appears that the spurless petals of A. ecalcarata cease cell divisions and enter the cell differentiation phase at an earlier developmental time point than those that produce spurs. This much more tractable list of 35 candidates genes will greatly facilitate targeted functional studies to assess the genetic control and evolution of petal spurs in Aquilegia.

Project description:Plant species aboveground allometry can be viewed as a functional trait that reflects the evolutionary trade-off between above- and belowground resources. In forest trees, allometry is related to productivity and resilience in different environments, and it is tightly connected with a compromise between efficiency-safety and competitive ability. A better understanding on how this trait varies within and across species is critical to determine the potential of a species/population to perform along environmental gradients. We followed a hierarchical framework to assess tree height-diameter allometry variation within and across four common European Pinus species. Tree height-diameter allometry variation was a function of solely genetic components -approximated by either population effects or clinal geographic responses of the population's site of origin- and differential genetic plastic responses -approximated by the interaction between populations and two climatic variables of the growing sites (temperature and precipitation)-. Our results suggest that, at the species level, climate of the growing sites set the tree height-diameter allometry of xeric and mesic species (Pinus halepensis, P. pinaster and P. nigra) apart from the boreal species (P. sylvestris), suggesting a weak signal of their phylogenies in the tree height-diameter allometry variation. Moreover, accounting for interpopulation variability within species for the four pine species aided to: (1) detect genetic differences among populations in allometry variation, which in P. nigra and P. pinaster were linked to gene pools -genetic diversity measurements-; (2) reveal the presence of differential genetic variation in plastic responses along two climatic gradients in tree allometry variation. In P. sylvestris and P. nigra, genetic variation was the result of adaptive patterns to climate, while in P. pinaster and P. halepensis, this signal was either weaker or absent, respectively; and (3) detect local adaptation in the exponent of the tree height-diameter allometry relationship in two of the four species (P. sylvestris and P. nigra), as it was a function of populations' latitude and altitude variables. Our findings suggest that the four species have been subjected to different historical and climatic constraints that might have driven their aboveground allometry and promoted different life strategies.

Dataset Information

Comparative Transcriptomics Among Four White Pine Species.

Publications

Comparative Transcriptomics Among Four White Pine Species.

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